Yeah I definitely agree with you on that point, though I've said before this isn't really a BiS for gearing. This is purely for theorycrafting and goal-setting purposes, and building your sets from. In no way do I think anyone will get full Thunderforged, double upgraded heroic pieces including the ones from Ra-den, except maybe the top elite boomkins who would have no use for this thread. Instead, it's to show what we have the possibility of attaining, and give a general idea of the items that go best together - this is why I don't give each piece their own DPS weight, because as you and others' have said, each item will interact with the others depending on their stat allocations and such.
So while people gear themselves up and they are more so just taking what's dropping rather than waiting for the best stuff, they should be importing themselves into WrathCalcs and checking what's best on an item-by-item basis, along with some thought on their part. If two pieces are almost exactly the same in terms of DPS reported by WrathCalcs, then you'd most likely go for the piece with higher crit to emphasise the importance of crit for multi-dotting. Conversely, if you're working on a fight with high movement and only one target, maybe you'd want to change your talents. Like you've said, we still need to use a bit of intuition when using models like WrathCalcs, and it's why when I compare items by hand I take 1 crit = 1.5 haste in order to emulate more of a multi-dotting scenario.
---------- Post added 2013-04-16 at 08:09 PM ----------
You may well be right - one of the shortcomings of WrathCalcs is that it doesn't take into account the stacking of procs and such, only Incarnation/CA/NV/potion/engineering gloves (I think gloves, not 100% sure). Heroism and the like has always been an average of its proc, so stacking is only emphasised in practice. We're still only talking about the initial burst for Breath vs. Cha-Ye's, but it may well come out to average higher than Cha-Ye's in the long run, depending on fight length.